As Ibrahim Baradiya recounts the events surrounding the last moments of his daughter's life at the bottom of a dark well, the agony of grief is drawn across the face of his wife, Fatima. She says almost nothing. Her eyes are half-closed. She shakes her head with small, rapid movements. A deep frown furrows her forehead. When the story is finished, she fetches her daughter's trinkets – beads, bangles, a hair clasp, a key ring, a purple pom-pom – and spreads them over the table and she weeps.

The story of Aya Baradiya's murder is like an incomplete jigsaw puzzle whose full picture may never be known; a dark and disturbing tale of death, lies, rumour, ruptured family relations, shame, despair and anger.

But the killing went far beyond a family affair. After the discovery of Aya's body more than a year after the 20-year-old university student went missing, her uncle confessed to Palestinian police, claiming it was an "honour" killing. Widespread protests against such crimes, led by students and women's organisations, erupted. In response, the Palestinian president last month scrapped historic laws that permitted leniency for the perpetrators of so-called "honour" killings.

Aya's father – a 56-year-old carpenter who works long hours to pay for the education of his 12 surviving children, five of whom are at university – begins the story with the day Aya went missing: 20 April 2010.

She left the family home in the West Bank town of Surif for an exam in English Literature at the nearby Hebron university. When she didn't return, Ibrahim and Fatima notified the police that she was missing and an investigation was launched.

Then the rumours began. Ibrahim heard variously that she was married, or had been spotted "in Ramallah, Nablus, Qalqilya, Jenin, Israel". Every time he heard of a possible sighting, Ibrahim went to look for his daughter, distributing photographs. At the time, the family never suspected Aya was dead.

Ibrahim now believes those rumours were all put about by his brother Okab, 37, currently in custody awaiting sentence for Aya's murder. "Okab said she had sent an SMS saying she was afraid to come back. All the rumours were spread by him. He tried to divert the security services."

In the previous months, Aya had received a marriage proposal from a man 17 years her senior. At first, worried about the age difference, Ibrahim had refused permission. "He came in an official way to ask, he did it properly. My daughter convinced me and then I agreed, but I said she could not marry until after her studies."

Aya's suitor was held by police for 35 days following her disappearance. Ibrahim begged him to reveal any information he had about her whereabouts. "He said: 'I don't know where she is. But your daughter disappeared after being with her uncle.'"

According to the family's account, Okab took Aya to his home a few days before her disappearance. While his wife was out, Okab made Aya coffee, they used the computer and Okab took a shower. Until Aya vanished, Ibrahim says his relationship with his brother was good. "After Aya disappeared, they stopped visiting. Even my sisters stopped coming. They were insulting my wife, saying: 'Now your daughter has run away, who will come and ask for your other daughters in marriage?'"

The suggestion that Aya had brought shame to her family's reputation had a powerful impact within conservative Palestinian society. The family was ostracised by their neighbours; Fatima rarely left the house during the 13 months between her daughter's disappearance and the discovery of her body.

Ibrahim, Fatima and their other children, whose ages range from four to 29, were distraught at Aya's disappearance, but they never gave up hope. However, says Ibrahim: "It was very hard for us. We were living in hell."

Then, last month, bones were discovered by chance in a well about four miles from the family home. Initially, it wasn't clear whether the remains were human or animal. "Even when the police in Hebron said it was a human body, I didn't think it was my daughter. I never thought she had been murdered."

But the police also found Aya's identity papers in a bag. Ibrahim and three of his sons were called to identify the remains. "We collapsed," he says.

The police went to the family home to give Fatima the devastating news as Ibrahim and other male family members were held for questioning – "harsh interrogation" – for three days. Ibrahim and his adult sons were released when Okab confessed to killing Aya. Okab and his accomplices had put a plastic bag over the young woman's head and thrown her, alive, to the bottom of the well. According to reports, he told police that he disapproved of her relationship with her fiance.

Aya's murder was immediately branded an "honour" killing. Under a 1960 Jordanian penal code, part of which still applies in the West Bank, which Jordan ruled between 1948 and 1967, perpetrators of such crimes are treated with leniency as they are deemed to have mitigating circumstances. The maximum sentence is six months, according to police. A clause in a 1936 British Mandate law, still in effect in Gaza, also allows for leniency in the punishment of "honour" killings.

Reliable statistics are hard to come by, but it is thought there are around 20 such crimes in the West Bank and Gaza each year. Women who have been raped or molested, or are victims of incest, are considered to have stained a family's reputation. Such acts of violation are rarely admitted by the victim's family.

Following the discovery of Aya's remains, 20,000 people attended her funeral, Ibrahim says. "They knew how innocent she was, they were demanding death for the criminals." There were protests against the "honour" killing laws at Hebron university, and Aya was commemorated as a "martyr".

During a live Palestinian television programme on Aya's case, a government official called in to say President Mahmoud Abbas was watching and intended to change the law. Abbas, who later met with Aya's family, signed the decree last month.

Pressure for a change in the law had been building before Aya's death. "The Palestinian women's movement has been struggling for many years on so-called 'honour' killings," says Amal Khreishe of the Palestinian Working Woman Society for Development. Her organisation submitted a petition signed by 8,000 women to the president's office this March demanding new legislation.

"We sent a message to the president that this is the time to cancel the articles in the penal law which encourage people to kill women and ignore the human rights and dignity of women," says Khreishe. She welcomes the president's move, but says it is a small step and "more political will is needed to enhance gender equality".

In Surif, Yasmine Alheeh, 29, minding a clothes shop, says she approves of the legal change. "There are a lot of things that are hard for a woman to do [in Palestinian society]. A woman has no personal freedom. It's OK to work, but you can't make personal choices."

Nearby, in a vegetable shop, Jalal Danah, 25, says women's actions are limited by Islam. "Our religion does not allow a woman to go out and practise her life without restriction. This would lead to corruption," he says.

Ibrahim Baradiya believes Okab and his accomplices "should be thrown in a well to suffer the same as my daughter suffered". He approves of the president's change to the law, but knows that it cannot bring Aya back nor heal his family rifts. Even his youngest daughter, Ranim, four, notices her mother's grief – her insomnia, dramatic weight loss and weeping – he says. "[My brother] stole part of me and part of my wife. He has destroyed the whole family."